You need to have "Cydia" or "Installer" on your iphone. Both of which you can get while jailbreaking. Unfortunately, thats the only way of installing them.
Otherwise, it is possible to SSH into your phone and manually some apps, but it can be a pain.
Depends on what the apps are. Some may be housed in other repositories that you may not have installed in Cydia. You'll basically gonna have to do some research on the apps.